The problem with pdb2pqr have been solved :)
Another question which I have is the calculation of the potential maps
from the ensemble of the conformers (for example I want to compare
potential distribution from the ensemble of the x-ray structures of one
protein which were solved in different condition).
In the visualization tab I found that APBS-2 can align maps. But what is
the most suitable way to provide such ensemble for the calculations ?
Should it be in NMR-like format or each conformer should be loaded by means
of poadDir for instance ? How I can calculate maps from all conformers at
once ?
James
2013/3/28 James Starlight
> by the way have someone had problems with the pdb2pqr usage with APBS in
> pymol?
>
>
> I've tried to install pdb2pqr from source as well as via packages
> then I've add usr/bin/pdb2pqr to the APBs plugin window
>
> and when I've started APBS I obtained error like
>
> Error: 5
> Exception in Tk callback
> Function: at 0x333fcf8> (type: )
> Args: ()
> Traceback (innermost last):
> File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
> line 1747, in __call__
> return apply(self.func, args)
> File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py",
> line 153, in
> command=lambda self=self, name=name: self._doCommand(name))
> File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py",
> line 132, in _doCommand
> return command(name)
> File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py",
> line 1036, in execute
> good = self.generatePqrFile()
> File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py",
> line 1007, in generatePqrFile
> good = self._generatePdb2pqrPqrFile()
> File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py",
> line 1615, in _generatePdb2pqrPqrFile
> if retval != 0:
> : local variable 'retval'
> referenced before assignment
>
> If I launch pdb2pqr from the terminal I've obtained
>
> own@starlight ~/Desktop $ pdb2pqr
> Usage: pdb2pqr.py [options] PDB_PATH PQR_OUTPUT_PATH
>
> pdb2pqr.py: error: Incorrect number (0) of arguments!
> argv: ['/usr/share/pdb2pqr/pdb2pqr.py'], args: []
>
> should I provide some addition paths to the bash?
> James
>
> 2013/3/27 James Starlight :
> > As I understood the APBs plugin which already exist in PyMol is the
> > very efficient device for electrostatic potential calculations.
> >
> > 2 questions have been arisen:
> >
> >
> > 1- How I could change cut-off distances for the electrostatic? E.g I'd
> > like to consider only interactions within 5 A between any charged
> > groups.
> >
> >
> > 2- What advantages has the usage of pdb2pqr plugin? Also in the
> > pdb2pqr tools options I've found some options for force fields. As I
> > know Poisson-Boltzmann equation on which APBS is based doesnt need any
> > force fields (charge calculation from ab initio principles). Why force
> > fields used here ?
> >
> > 3- IS there other plugins for the electrostatic surface calculation
> > with (1) possibility to change cut-offs and (2) charge assignment from
> > the force fields or ab initio calculations ?
> >
> >
> > Thanks for help,
> > James
> >
> > 2013/3/27 Mike Marchywka :
> >>
> >>
> >>
> >> I have a similar requirement, taking density and potential
> dstriutbutions from
> >> jdftx which are written as plain binarry doubles. I use a script and
> >> some code to create an xplor file which seems to work but I have
> >> to adjust the position and scale to let it
> >> overlay the ion positions that I read from an xyz file.
> >>
> >> AFAICT xplor is about the only easy format that pymol takes
> >> but I was debating about trying to find others. i think
> >> I dug through my older version of pymol, went to the
> >> effort of changing it all to c++/extern c and then dropped it.
> >> The xplor approch seems to work well enough for now.
> >>
> >>
> >> Is there an easier way?
> >> Thanks.
> >>
> >>
> >>
> >>> Date: Wed, 27 Mar 2013 13:41:24 +0400
> >>> From: jmsstarli...@gmail.com
> >>> To: pymol-users@lists.sourceforge.net
> >>> Subject: [PyMOL] Electrostatic potential surface
> >>>
> >>> Dear PyMol users!
> >>>
> >>>
> >>> I wounder to know about built-in PyMol option for electrostatic
> >>> potential visualisation.
> >>>
> >>> For example I have pdb coordinates of my protein as well as its
> >>> electrostatic potential distribution (calculated by another software).
> >>> Using MolMol with both of that files I can visualize the electrostatic
> >>> potential surface by means of "PaintSurface" option. Can I do the same
> >>> with the PyMOl?
> >>>
> >>>
> >>>
> >>> Thanks for help,
> >>>
> >>>
> >>> James
> >>>
> >>>
> --
> >>> Own the Future-Intel® Level Up Game Demo Contest 2013
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